Several high resolution molecular genetic techniques have been successful in identifying and localizing chromosomal defects in solid tumors. However, researchers have been largely unsuccessful in finding consistent defects in prostatic adenocarcinoma (CaP) and benign prostatic hypertrophy (BPH). A relatively new application of the conventional RFLP technique, DNA fingerprinting, has shown some promise in revealing differences between tumor and normal DNA. We have used this technology to screen 14 examples of CaP and 12 examples of BPH. Seventy percent of carcinomas screened had evidence of chromosomal alterations. Unexpectedly, 33% of BPH samples exhibited detectable changes also. The genetic rearrangements may be important markers for the carcinoma, while those detected in BPH may precede those in CaP.